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Genome Sequence of a Novel Archaeal Fusellovirus Assembled from
the Metagenome of a Mexican Hot Spring
Luis E. Servín-Garcidueñas,a Xu Peng,b Roger A. Garrett,b Esperanza Martínez-Romeroa
Department of Ecological Genomics, Center for Genomic Sciences, National University of Mexico, Cuernavaca, Morelos, Mexicoa; Department of Biology, Archaea Centre,
University of Copenhagen, Copenhagen, Denmarkb
The consensus genome sequence of a new member of the family Fuselloviridae designated as SMF1 (Sulfolobales Mexican fusellovirus 1) is presented. The complete circular genome was recovered from a metagenomic study of a Mexican hot spring. SMF1
exhibits an exceptional coding strand bias and a reduced set of fuselloviral core genes.
Received 5 March 2013 Accepted 15 March 2013 Published 25 April 2013
Citation Servín-Garcidueñas LE, Peng X, Garrett RA, Martínez-Romero E. 2013. Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a
Mexican hot spring. Genome Announc. 1(2):e00164-13. doi:10.1128/genomeA.00164-13.
Copyright © 2013 Servín-Garcidueñas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Luis E. Servín-Garcidueñas, [email protected].
M
embers of the Fuselloviridae family from the crenarchaeal
order Sulfolobales have been characterized, and they are
abundant in extreme geothermal environments (1, 2). They carry
circular double-stranded DNA (dsDNA) genomes and exhibit
spindle-shaped morphologies. Here, we report the consensus genome sequence of a novel fusellovirus recovered from aqueous
sediments from Los Azufres, Mexico.
Samples were collected from a hot spring with a pH of 3.6 and
a temperature of 65°C. DNA was purified using the UltraClean
microbial and the UltraClean Mega soil DNA kits (MoBio Laboratories, Inc., Carlsbad, CA). Sequencing was performed on an
Illumina GAIIx platform, producing 36-bp paired-end reads with
300-bp inserts representing 216 Mb. Reads were assembled using
Velvet 1.2.07 (3). A set of contigs were predicted by BLASTX
searches to be of fuselloviral origin. Gaps were closed iteratively by mapping and reassembling reads to these contigs using Maq 0.7.1 (4) and Velvet. Open reading frames (ORFs)
were predicted using GeneMark.hmm2.0 (5) and were manually verified using Artemis (6).
The average sequence coverage of the 14,847-bp circular
dsDNA genome was 1,257-fold. We detected 57 candidate single
nucleotide polymorphisms by Maq. The G⫹C content was
45.43%, higher than the 37.5 to 39.7% content of other fuselloviral
genomes (1, 2, 7–9).
The genome has a strong coding-strand bias, not previously
seen for fuselloviruses, with only the ubiquitous fuselloviral
integrase encoded on one strand. The gene organization is also
exceptional for fuselloviruses, with a high incidence of genes
arranged in operons, which are also likely to encode cofunctional proteins.
Twenty-four genes were predicted, 22 of which are arranged in
five operons. Fourteen genes have putative fuselloviral homologs,
consistent with SMF1 being a member of the Fuselloviridae family.
Most gene products show 30 to 70% amino acid sequence similarity to the best fuselloviral matches. Previous studies identified thirteen genes conserved in all fusellovirus genomes (2),
March/April 2013 Volume 1 Issue 2 e00164-13
and nine of these were localized in a “core” genomic region of
SMF1. The core genes encode a DnaA-like protein, the integrase, one VP1-like structural protein, a putative helix-turnhelix (HTH) transcriptional regulator, and five proteins with
unknown functions.
Five additional putative gene products shared with other fuselloviruses include a second VP1-like protein, a VP2-like structural protein, a putative end-filament protein, a regulatory protein, and a hypothetical protein. Three further nonconserved ORF
products showed sequence similarities to putative regulatory proteins.
The host of SMF1 is likely to be a member of the order Sulfolobales. Fuselloviruses can replicate in both Sulfolobus and Acidianus
species of the order Sulfolobales (2), and they are predicted to have
an extended host range that may include as-yet-uncultured species (10).
In conclusion, the SMF1 genome was recovered from a site
widely separated geographically from the locations of other sequenced fuselloviruses. The SMF1 genome shows exceptional
properties, including a coding-strand bias and a high incidence of
genes organized in operon structures, but nevertheless, it retains a
large set of conserved fusellovirus genes, which lends further support to the exchange of genetic material over intercontinental distances (2, 10).
Nucleotide sequence accession number. The genome sequence
was deposited in GenBank under the accession no. KC618393.
ACKNOWLEDGMENTS
This research was supported by PAPIIT IN205412 from DGAPA, UNAM,
and by SUBNARGEM, SAGARPA. L.E.S.G. received a PhD scholarship
from CONACYT (Mexico). L.E.S.-G. had a “Beca Mixta” from
CONACYT and a fellowship from PAEP during a research internship at
the Danish Archaea Center.
We thank the Programa de Doctorado en Ciencias Biomédicas from
UNAM, the UUSM from UNAM for sample sequencing, and Jesús Campos García from the UMSNH for providing laboratory facilities. The CFE
personnel provided a permit for samplings.
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Servín-Garcidueñas et al.
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Genome Announcements
March/April 2013 Volume 1 Issue 2 e00164-13